Assessing the reproducibility of discriminant function analyses.

Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. Even if data files are securely stored and accessible, they must also be accompanied by accurate labels and identifiers. To assess how often problems with metadata or data curation affect the reproducibility of published results, we attempted to reproduce Discriminant Function Analyses (DFAs) from the field of organismal biology. DFA is a commonly used statistical analysis that has changed little since its inception almost eight decades ago, and therefore provides an opportunity to test reproducibility among datasets of varying ages. Out of 100 papers we initially surveyed, fourteen were excluded because they did not present the common types of quantitative result from their DFA or gave insufficient details of their DFA. Of the remaining 86 datasets, there were 15 cases for which we were unable to confidently relate the dataset we received to the one used in the published analysis. The reasons ranged from incomprehensible or absent variable labels, the DFA being performed on an unspecified subset of the data, or the dataset we received being incomplete. We focused on reproducing three common summary statistics from DFAs: the percent variance explained, the percentage correctly assigned and the largest discriminant function coefficient. The reproducibility of the first two was fairly high (20 of 26, and 44 of 60 datasets, respectively), whereas our success rate with the discriminant function coefficients was lower (15 of 26 datasets). When considering all three summary statistics, we were able to completely reproduce 46 (65%) of 71 datasets. While our results show that a majority of studies are reproducible, they highlight the fact that many studies still are not the carefully curated research that the scientific community and public expects

Temperature effects on Florida applesnail activity: implications for snail kite foraging success and distribution

The endangered Florida snail kite (Rostrhamlls sociaiJilis) feeds exclusively on applesnails (Pomacea pailiclosa), yet we lack direct observations that link applesnail behavior to snail kite foraging success. The purpose of our study was to evaluate the temperature-activity profile of applesnails in the context of restricted foraging opportunities for snail kites. Applesnail activity was monitored in water temperatures ranging from 2-2

BCAS: A Web-enabled and GIS-based Decision Support System for the Diagnosis and Treatment of Breast Cancer

For decades, geographical variations in cancer rates have been observed but the precise determinants of such geographic differences in breast cancer development are unclear. Various statistical models have been proposed. Applications of these models, however, require that the data be assembled from a variety of sources, converted into the statistical models’ parameters and delivered effectively to researchers and policy makers. A web-enabled and GIS-based system can be developed to provide the needed functionality. This article overviews the conceptual web-enabled and GIS-based system (BCAS), illustrates the system’s use in diagnosing and treating breast cancer and examines the potential benefits and implications for breast cancer research and practice

Results at 24 months from the prospective, randomized, multicenter Investigational Device Exemption trial of ProDisc-C versus anterior cervical discectomy and fusion with 4-year follow-up and continued access patients.

BackgroundCervical total disk replacement (TDR) is intended to address pain and preserve motion between vertebral bodies in patients with symptomatic cervical disk disease. Two-year follow-up for the ProDisc-C (Synthes USA Products, LLC, West Chester, Pennsylvania) TDR clinical trial showed non-inferiority versus anterior cervical discectomy and fusion (ACDF), showing superiority in many clinical outcomes. We present the 4-year interim follow-up results.MethodsPatients were randomized (1:1) to ProDisc-C (PDC-R) or ACDF. Patients were assessed preoperatively, and postoperatively at 6 weeks and 3, 6, 12, 18, 24, 36, and 48 months. After the randomized portion, continued access (CA) patients also underwent ProDisc-C implantation, with follow-up visits up to 24 months. Evaluations included Neck Disability Index (NDI), Visual Analog Scale (VAS) for pain/satisfaction, and radiographic and physical/neurologic examinations.ResultsRandomized patients (103 PDC-R and 106 ACDF) and 136 CA patients were treated at 13 sites. VAS pain and NDI score improvements from baseline were significant for all patients (P < .0001) but did not differ among groups. VAS satisfaction was higher at all time points for PDC-R versus ACDF patients (P = .0499 at 48 months). The percentage of patients who responded yes to surgery again was 85.6% at 24 months and 88.9% at 48 months in the PDC-R group, 80.9% at 24 months and 81.0% at 48 months in the ACDF group, and 86.3% at 24 months in the CA group. Five PDC-R patients (48 months) and no CA patients (24 months) had index-level bridging bone. By 48 months, approximately 4-fold more ACDF patients required secondary surgery (3 of 103 PDC-R patients [2.9%] vs 12 of 106 ACDF patients [11.3%], P = .0292). Of these, 6 ACDF patients (5.6%) required procedures at adjacent levels. Three CA patients required secondary procedures (24 months).ConclusionsOur 4-year data support that ProDisc-C TDR and ACDF are viable surgical options for symptomatic cervical disk disease. Although ACDF patients may be at higher risk for additional surgical intervention, patients in both groups show good clinical results at longer-term follow-up

Incidence and time course of everolimus-related adverse events in postmenopausal women with hormone receptor-positive advanced breast cancer: insights from BOLERO-2.

BackgroundIn the BOLERO-2 trial, everolimus (EVE), an inhibitor of mammalian target of rapamycin, demonstrated significant clinical benefit with an acceptable safety profile when administered with exemestane (EXE) in postmenopausal women with hormone receptor-positive (HR(+)) advanced breast cancer. We report on the incidence, time course, severity, and resolution of treatment-emergent adverse events (AEs) as well as incidence of dose modifications during the extended follow-up of this study.Patients and methodsPatients were randomized (2:1) to receive EVE 10 mg/day or placebo (PBO), with open-label EXE 25 mg/day (n = 724). The primary end point was progression-free survival. Secondary end points included overall survival, objective response rate, and safety. Safety evaluations included recording of AEs, laboratory values, dose interruptions/adjustments, and study drug discontinuations.ResultsThe safety population comprised 720 patients (EVE + EXE, 482; PBO + EXE, 238). The median follow-up was 18 months. Class-effect toxicities, including stomatitis, pneumonitis, and hyperglycemia, were generally of mild or moderate severity and occurred relatively early after treatment initiation (except pneumonitis); incidence tapered off thereafter. EVE dose reduction and interruption (360 and 705 events, respectively) required for AE management were independent of patient age. The median duration of dose interruption was 7 days. Discontinuation of both study drugs because of AEs was higher with EVE + EXE (9%) versus PBO + EXE (3%).ConclusionsMost EVE-associated AEs occur soon after initiation of therapy, are typically of mild or moderate severity, and are generally manageable with dose reduction and interruption. Discontinuation due to toxicity was uncommon. Understanding the time course of class-effect AEs will help inform preventive and monitoring strategies as well as patient education.Trial registration numberNCT00863655

Predictive factors for ovarian response in a corifollitropin alfa/GnRH antagonist protocol for controlled ovarian stimulation in IVF/ICSI cycles

Background This secondary analysis aimed to identify predictors of low (<6 oocytes retrieved) and high ovarian response (>18 oocytes retrieved) in IVF patients undergoing controlled ovarian stimulation with corifollitropin alfa in a gonadotropin-releasing hormone (GnRH) antagonist protocol. Methods Statistical model building for high and low ovarian response was based on the 150 μg corifollitropin alfa treatment group of the Pursue trial in infertile women aged 35–42 years (n = 694). Results Multivariable logistic regression models were constructed in a stepwise fashion (P <0.05 for entry). 14.1 % of subjects were high ovarian responders and 23.2 % were low ovarian responders. The regression model for high ovarian response included four independent predictors: higher anti-Müllerian hormone (AMH) and antral follicle count (AFC) increased the risk, and higher follicle-stimulating hormone (FSH) levels and advancing age decreased the risk of high ovarian response. The regression model for low ovarian response also included four independent predictors: advancing age increased the risk, and higher AMH, higher AFC and longer menstrual cycle length decreased the risk of low ovarian response. Conclusions AMH, AFC and age predicted both high and low ovarian responses, FSH predicted high ovarian response, and menstrual cycle length predicted low ovarian response in a corifollitropin alfa/GnRH antagonist protocol